Even though I cannot reproduce this issue, please do not close it as incomplete. Because I know it is incomplete, I tried e-mailing it to support, and they told me to take it here.

Even though these aren't reliable reproduction steps, it is information about the conditions under which the issue happened. It is my hope that people can pool their knowledge and experiences and we can find out more. Failing that, the developers know the source code and may very well have a theory as to the cause anyway.

Here is the story:

• I made a portal and went to the Nether and back a few times. No problem.

• I built a cobblestone room around the portal on the Nether side using bottom-half slabs for the floor and ceiling. Also adjacent to the portal was a door leading to some stairs heading downward to a rear entrance/exit.

• Upon returning to the Overworld, I exited through a second portal that had been spontaneously created (the one on the left). No matter which portal was used to get to the Nether, this portal was always the exit portal going forward.

• Many days go by. A creeper manages to get through a portal to the Nether and blows up six slabs in front of the portal on the Nether side.

• The next time I portal to the Nether, I exit through another spontaneously generated portal: The one on the roof.

• Now, even after repairing the floor, the one on the roof is the only portal that brings me to the Nether. My two original portals are completely nonfunctional as exit portals.

Also note that the portals can be mined and abused for infinite obsidian.